LamBras's md [61 articles] Export

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	Sulfide-Binding Hemoglobins: Effects of Mutations on Active-Site Flexibility [My Copy] Biophysical Journal, Vol. 91, No. 5. (01 September 2006), pp. 1698-1709. by S. Fernandezalberti, D. Bacelo, R. Binningjr, J. Echave, M. Chergui, J. Lopezgarriga posted to flexibility md by LamBras on 2009-03-13 18:38:22 as
	Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. [My Copy] Journal of molecular graphics & modelling, Vol. 16, No. 4-6. (c 1998) by J. Marelius, K. Kolmodin, I. Feierberg, J. Aqvist posted to md by LamBras on 2009-03-11 17:49:50 as along with 1 person npt11tpn
	Recent advances in the development and application of implicit solvent models in biomolecule simulations [My Copy] Current Opinion in Structural Biology, Vol. 14, No. 2. (April 2004), pp. 217-224. by M. Feig posted to md by LamBras on 2009-03-11 12:18:05 as along with 6 people and 2 groups flbarroso apostola ttjoseph marcius gane5h RamuAnandakrishnan BioinfoCIPF SGU-CIPF
	Electrostatics calculations: latest methodological advances. [My Copy] Current opinion in structural biology, Vol. 16, No. 2. (13 April 2006), pp. 142-151. by Patrice Koehl posted to md by LamBras on 2009-03-11 12:09:42 as along with 7 people oteri r2s2 flbarroso BragilMassoud qwermish RamuAnandakrishnan jteyra
	Dynamics of folded proteins. [My Copy] Nature, Vol. 267, No. 5612. (16 June 1977), pp. 585-590. by J. A. McCammon, B. R. Gelin, M. Karplus posted to md by LamBras on 2009-03-11 11:51:35 as along with 1 person dfgreen
	The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin [My Copy] Journal of the American Chemical Society, Vol. 110, No. 6. (1 March 1988), pp. 1657-1666. by William L. Jorgensen, Julian Tirado-Rives posted to forcefield md by LamBras on 2008-12-20 17:23:28 as along with 1 person dfgreen
	Structure and dynamics of the full-length M1 muscarinic acetylcholine receptor studied by molecular dynamics simulations [My Copy] Archives of Biochemistry and Biophysics, Vol. 469, No. 1. (01 January 2008), pp. 142-150. by L. Espinozafonseca, A. Pedretti, G. Vistoli posted to alzheimer m1m2 md by LamBras on 2008-12-15 12:58:48 as
	Calculation of absolute protein-ligand binding free energy from computer simulations. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6825-6830. by H. J. Woo, B. Roux posted to forcefield free_energy md by LamBras on 2008-09-25 08:44:20 as along with 4 people flbarroso ibuch ttjoseph ashaytan
	Involvement of Water in Carbohydrate-Protein Binding [My Copy] J. Am. Chem. Soc., Vol. 123, No. 49. (12 December 2001), pp. 12238-12247. by C. Clarke, R. J. Woods, J. Gluska, A. Cooper, M. A. Nutley, G. J. Boons posted to free_energy itc md water_replacement by LamBras on 2008-09-24 16:23:00 as
	Role of protein flexibility in the design of Bcl-X(L) targeting agents: insight from molecular dynamics. [My Copy] Journal of computer-aided molecular design (9 September 2008) by William Novak, Hongming Wang, Goran Krilov posted to flexibility free_energy md by LamBras on 2008-09-16 12:47:10 as along with 2 people paulschlesinger higueruelo
	Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied? [My Copy] J. Chem. Theory Comput., Vol. 3, No. 4. (10 July 2007), pp. 1550-1560. by D. R. Nutt, J. C. Smith posted to md by LamBras on 2008-08-11 21:06:20 as along with 3 people barmak7282 onufriev softsimu
	Advances in biomolecular simulations: methodology and recent applications. [My Copy] Quarterly reviews of biophysics, Vol. 36, No. 3. (August 2003), pp. 257-306. by J. Norberg, L. Nilsson posted to md review by LamBras on 2008-08-11 20:53:21 as along with 3 people flbarroso baaden ltrabuco
	Biomolecular modeling: Goals, problems, perspectives. [My Copy] Angewandte Chemie (International ed. in English), Vol. 45, No. 25. (19 June 2006), pp. 4064-4092. by Wilfred F. van Gunsteren, Dirk Bakowies, Riccardo Baron, et al.Indira Chandrasekhar, Markus Christen, Xavier Daura, Peter Gee, Daan P. Geerke, Alice Glättli, Philippe H. Hünenberger, Mika A. Kastenholz, Chris Oostenbrink, Merijn Schenk, Daniel Trzesniak, Nico F. van der Vegt, Haibo B. Yu posted to md review by LamBras on 2008-08-11 20:51:57 as along with 2 people mijogiffin patricia
	Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins [My Copy] Chemical Reviews, Vol. 106, No. 5. (1 May 2006), pp. 1589-1615. by Stewart A. Adcock, J. Andrew Mccammon posted to md review by LamBras on 2008-08-11 20:50:31 as along with 5 people flbarroso yxue tovrstra aqeel higueruelo
	Normal Modes and Essential Dynamics [My Copy] Molecular Modeling of Proteins, Vol. 443 (2008), pp. 89-106. by Steven Hayward, Bert L. Groot posted to md normal_modes by LamBras on 2008-07-24 12:31:31 as along with 4 people and 1 group arybakov ruvido csrocha higueruelo structural_bioinformatics
	Molecular dynamics simulations of ethanol binding to the transmembrane domain of the glycine receptor: Implications for the channel potentiation mechanism [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Mary H. Cheng, Rob D. Coalson, Michael Cascio posted to md by LamBras on 2008-07-20 16:15:14 as along with 1 person RamuAnandakrishnan
	Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2 Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA [My Copy] Biochemistry, Vol. 44, No. 9. (8 March 2005), pp. 3410-3417. by E. R. Valentine, A. G. Palmer posted to dynamics ion_channels md by LamBras on 2008-07-20 15:33:56 as along with 1 person rph
	A dynamic model for the allosteric mechanism of GroEL. [My Copy] J Mol Biol, Vol. 302, No. 2. (15 September 2000), pp. 303-313. by J. Ma, P. B. Sigler, Z. Xu, M. Karplus posted to md targeted_md by LamBras on 2008-07-20 15:11:27 as along with 3 people dfgreen lna dgront
	Molecular Dynamics Simulations of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor GluR2 [My Copy] Biophys. J., Vol. 82, No. 2. (1 February 2002), pp. 676-683. by Yalini Arinaminpathy, Mark S. Sansom, Philip C. Biggin posted to md nmda by LamBras on 2008-07-20 15:06:57 as
	Molecular dynamics simulations of biomolecules. [My Copy] Nat Struct Biol, Vol. 9, No. 9. (September 2002), pp. 646-652. by M. Karplus, J. A. McCammon posted to md review by LamBras on 2008-07-17 18:05:33 as along with 8 people saravan yxue onufriev adilson_mohr yalexeev baaden aqeel RamuAnandakrishnan
	Targeted molecular dynamics simulation studies of binding and conformational changes in <I>E. coli</I> MurD [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 1. (2007), pp. 243-254. by Andrej Perdih, Miha Kotnik, Milan Hodoscek, Tom Solmajer posted to md targeted_md by LamBras on 2008-07-17 18:00:23 as
	Extending the capabilities of targeted molecular dynamics: Simulation of a large conformational transition in plasminogen activator inhibitor 1 [My Copy] Protein Sci, Vol. 10, No. 4. (1 April 2001), pp. 798-808. by Peter Kruger, Stefan Verheyden, Paul J. Declerck, Yves Engelborghs posted to md targeted_md by LamBras on 2008-07-17 17:58:24 as along with 1 person ruvido
	Targeted Molecular Dynamics Simulation of Conformational Change-Application to the T ↔ R Transition in Insulin [My Copy] Molecular Simulation, Vol. 10, No. 2. (1993), pp. 291-308. by J. Schlitter, M. Engels, P. Krüger, E. Jacoby, A. Wollmer posted to md targeted_md by LamBras on 2008-07-17 17:56:50 as
	Steered molecular dynamics investigations of protein function [My Copy] Journal of Molecular Graphics and Modelling, Vol. 19, No. 1. (February 2001), pp. 13-25. by Barry Isralewitz, Jerome Baudry, Justin Gullingsrud, Dorina Kosztin, Klaus Schulten posted to md targeted_md by LamBras on 2008-07-17 17:55:50 as along with 1 person choonpeng
	Steered molecular dynamics and mechanical functions of proteins [My Copy] Current Opinion in Structural Biology, Vol. 11, No. 2. (1 April 2001), pp. 224-230. by Barry Isralewitz, Mu Gao, Klaus Schulten posted to md targeted_md by LamBras on 2008-07-17 17:54:26 as along with 3 people and 2 groups devinli barry ttjoseph structural_bioinformatics Bioinformatics
	Targeted molecular dynamics: A new approach for searching pathways of conformational transitions [My Copy] Journal of Molecular Graphics, Vol. 12, No. 2. (June 1994), pp. 84-89. by J. Schlitter, M. Engels, P. Kruger posted to md targeted_md by LamBras on 2008-07-17 17:53:07 as along with 1 person cactus
	Computer simulations of protein folding by targeted molecular dynamics [My Copy] Proteins: Structure, Function, and Genetics, Vol. 39, No. 3. (2000), pp. 252-260. by Philippe Ferrara, Joannis Apostolakis, Amedeo Caflisch posted to md targeted_md by LamBras on 2008-07-17 17:51:25 as
	Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding [My Copy] J. Am. Chem. Soc., Vol. 130, No. 9. (5 March 2008), pp. 2817-2831. by R. Abel, T. Young, R. Farid, B. J. Berne, R. A. Friesner posted to free_energy md by LamBras on 2008-07-15 15:47:18 as
	An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. [My Copy] J Comput Aided Mol Des (15 January 2008) by Rommie E. Amaro, Riccardo Baron, J A. McCammon posted to docking flexibility md by LamBras on 2008-07-04 11:00:17 as along with 6 people and 2 groups karinaecomp oteri jmccammon rbaron higueruelo kazemi Structural Biology Group TorVergata McCammon
	Molecular dynamics simulations of LysRS: An asymmetric state [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 62, No. 3. (29 November 2005), 662. by S. J. Hughes, J. A. Tanner, A. D. Miller, I. R. Gould posted to md trna by LamBras on 2008-06-10 16:06:08 as
	Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation [My Copy] Current Opinion in Structural Biology In Catalysis and regulation / Proteins, Vol. 17, No. 6. (December 2007), pp. 633-640. by Ivet Bahar, Chakra Chennubhotla, Dror Tobi posted to allosteric flexibility md by LamBras on 2008-04-25 14:35:05 as along with 10 people and 4 groups allmensch jrperillaj barry aqeel ruvido cactus sobolevnrm jennifermbui higueruelo jmccammon structural_bioinformatics Bioinformatics baker-group McCammon
	A consensus view of protein dynamics [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 3. (16 January 2007), pp. 796-801. by Manuel Rueda, Carles Ferrer-Costa, Tim Meyer, et al.Alberto Pérez, Jordi Camps, Adam Hospital, Josep L. Gelpí, Modesto Orozco posted to md by LamBras on 2008-04-25 14:33:01 as along with 14 people and 1 group Diego_Prada bmduggan lna dimka aqeel aswin rabio grahamc hmk zwang biehl Ema phoenixzxl ras The BMM Dome
	Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models? [My Copy] BMC Bioinformatics, Vol. 9 (07 January 2008), 6. by Jean-Francois Taly, Antoine Marin, Jean-Francois Gibrat posted to md by LamBras on 2008-04-25 14:32:39 as along with 2 people and 1 group oteri biehl Structural Biology Group TorVergata
	Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein [My Copy] Journal of Computer-Aided Molecular Design by Ami Yang, Ricardo Mancera posted to flexibility md by LamBras on 2008-04-24 15:31:32 as along with 1 person zimbo1
	Mechanism of Na+/H+ Antiporting [My Copy] Science, Vol. 317, No. 5839. (10 August 2007), pp. 799-803. by Isaiah T. Arkin, Huafeng Xu, Morten O. Jensen, et al.Eyal Arbely, Estelle R. Bennett, Kevin J. Bowers, Edmond Chow, Ron O. Dror, Michael P. Eastwood, Ravenna Flitman-Tene, Brent A. Gregersen, John L. Klepeis, Istvan Kolossvary, Yibing Shan, David E. Shaw posted to md by LamBras on 2008-04-03 09:22:43 as along with 6 people and 1 group Diego_Prada allmensch sobolevnrm Jporci MMehrotra dimka baker-group
	Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins† [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 19. (1 May 2008), pp. 6155-6158. by Paul Maragakis, Kresten Lindorff-Larsen, Michael P. Eastwood, et al.Ron O. Dror, John L. Klepeis, Isaiah T. Arkin, Morten O. Jensen, Huafeng Xu, Nikola Trbovic, Richard A. Friesner, Arthur G. Palmer, David E. Shaw posted to md by LamBras on 2008-04-03 09:22:08 as along with 3 people and 1 group pavanghatty allmensch skoddet Nielsen group
	Force Field Validation Using Protein Side Chain Prediction [My Copy] J. Phys. Chem. B, Vol. 106, No. 44. (7 November 2002), pp. 11673-11680. by M. P. Jacobson, G. A. Kaminski, R. A. Friesner, C. S. Rapp posted to forcefield md sidechain by LamBras on 2008-03-22 16:09:35 as
	Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† [My Copy] The Journal of Physical Chemistry B, Vol. 105, No. 28. (1 July 2001), pp. 6474-6487. by George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, William L. Jorgensen posted to forcefield md by LamBras on 2008-03-22 16:06:30 as along with 1 person softsimu
	Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 2. (1 November 2007), pp. 684-694. by Nikola Trbovic, Byungchan Kim, Richard A. Friesner, Arthur G. Palmer posted to md nmr by LamBras on 2008-03-20 19:53:17 as
	Probing ligand binding modes of human cytochrome P450 2J2 by homology modeling, molecular dynamics simulation, and flexible molecular docking [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 2. (14 November 2007), pp. 938-949. by Weihua Li, Yun Tang, Hong Liu, Jiagao Cheng, Weiliang Zhu, Hualiang Jiang posted to docking homology_modeling md by LamBras on 2008-03-20 19:37:17 as
	Protein flexibility and dynamics using constraint theory [My Copy] J Mol Graph Model, Vol. 19, No. 1. (2001), pp. 60-69. by M. F. Thorpe, M. Lei, A. J. Rader, D. J. Jacobs, L. A. Kuhn posted to flexibility md by LamBras on 2008-03-15 16:27:11 as
	A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor [My Copy] J Comput Chem, Vol. 25, No. 16. (2004), pp. 1995-2005. by R. Tatsumi, Y. Fukunishi, H. Nakamura posted to flexibility hd md by LamBras on 2008-03-15 16:27:11 as
	Probing flexibility and ?induced-fit? phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 56, No. 1. (2004), pp. 52-66. by Christoph Sotriffer, Oliver Krã¤mer, Gerhard Klebe posted to docking flexibility md by LamBras on 2008-03-15 16:27:11 as
	Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms [My Copy] J. Chem. Theory Comput. (2007) by J. Shao, S. W. Tanner, N. Thompson, T. E. Cheatham posted to clustering md by LamBras on 2008-03-15 16:27:11 as
	Wordom: a program for efficient analysis of molecular dynamics simulations [My Copy] Bioinformatics, Vol. 23, No. 19. (2007), pp. 2625-2627. by Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch posted to md by LamBras on 2008-03-15 16:27:11 as
	Calculation of ligand binding free energies from molecular dynamics simulations [My Copy] International Journal of Quantum Chemistry, Vol. 69, No. 1. (1998), pp. 77-88. by J. Marelius, T. Hansson, J. Ã…qvist posted to free_energy md by LamBras on 2008-03-15 16:27:10 as
	Protein flexibility using constraints from molecular dynamics simulations [My Copy] Phys Biol, Vol. 2, No. 4. (2005) by T. Mamonova, B. Hespenheide, R. Straub, M. F. Thorpe, M. Kurnikova posted to flexibility md by LamBras on 2008-03-15 16:27:10 as
	Full correlation analysis of conformational protein dynamics [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007) by Oliver Lange, Helmut Grubmã¼ller posted to md normal_modes by LamBras on 2008-03-15 16:27:10 as
	Protein flexibility: its role in structure and mechanism revealed by molecular simulations [My Copy] Cell Mol Life Sci, Vol. 63, No. 2. (2006), pp. 207-219. by G. Dodson, C. S. Verma posted to flexibility md by LamBras on 2008-03-15 16:27:08 as
	Combining docking and molecular dynamic simulations in drug design [My Copy] Med Res Rev (2006) by Hernã¡n Alonso, Andrey A. Bliznyuk, Jill E. Gready posted to docking md by LamBras on 2008-03-15 16:27:08 as

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flexibility	61
md	61
nmda	58
serinracemase	58
docking	53
virtual_screening	45
adme	30
drugdesign	26
review	19
scoring	18
cheminformatics	14
trna	13
bayesian	12
free_energy	12
ion_channels	12
muscarinic	12
sidechain	12
library_design	10
homology_modeling	9
normal_modes	8
targeted_md	8
nr1	7
rotamers	7
sar	7
conformers	6
gpcr	6
clustering	5
forcefield	5
nmr	5
xray	5
druglike	4
herg	4
proteins	4
surface	4
water_replacement	4
alzheimer	3
chemicalspace	3
ensemble	3
fingerprints	3
hts	3
scaffoldhopping	3
correlation	2
dynamics	2
graph	2
hd	2
lipophilicity	2
mmpbsa	2
pipelining	2
racemase	2
shape	2
similarity	2
allosteric	1
denovo	1
de_novo	1
induced_fit	1
itc	1
m1m2	1
ppb	1
qsar	1
r1	1
schroedinger	1
validation	1
virtuak_screening	1
x-ray	1

LamBras's md [61 articles] Export

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